Did more testing and this is what i have found:
Steps to Replicate:
1. Create a lineup without a GAME CHANGER (GC) card.
2. Note one of the player in your lineup, in my case I used Michael Crabtree with a base stats of 85 spd, 88 jmp, and 72 str.
3. Change one of your player with a GC card, in my case I used Dee Milliner with + 2 jmp and - 1 spd.
4. Actual Result: Michael Crabtree's base stat did not change, it is still 85 spd and 88 jmp.
5. Check Michael Crabtree's BACK OF THE CARD stats, the stat was now 84 spd and 90 jmp.
6. Go back to the main window of the APPS.
7. Close Madden NFL mobile apps, If you are using apple devices - double click the home button and swipe up the apps.
8. Open Madden NFL mobile apps and go to the Manage Lineup window.
9. Check on Michael Crabtree's, the base stat is now 84 spd and 90 jmp.
10. Check on Michael Crabtree's BACK OF THE CARD stat - IT INCREASES TO 92 jmp and decreases to 83 spd. I suspect that the cause of it was because the base stat was updated, I hope this is just a GUI problem and not the stats perse that dictates the flow of the game.
The effect will be just the same EVERYTIME you include a game changer card on your lineup, the effect on THE BASE STATS WILL NOT SHOW UP not until you RESTART the apps. But once you do that, the BACK OF THE CARD stats will be modified twice.
The problem is this same even if you tap on the best lineup button, you still have to restart the apps. Also, if you are going to remove a GC card, the change will not take effect until you restart the apps.
This is definitely a problem, may it be an aesthetics or performance. For now, all I can contribute is to provide information on how to replicate the problem and a work around to solve it. Hopefully the EA TEAM can take a look on it and maybe provide a resolution regarding the problem you are having.